The Haplotype-Based Analysis of Aegilops tauschii Introgression Into Hard Red Winter Wheat and Its Impact on Productivity Traits

Abstract

The introgression from wild relatives have a great potential to broaden the availability of beneficial allelic diversity for crop improvement in breeding programs. Here, we assessed the impact of the introgression from 21 diverse accessions of Aegilops tauschii, the diploid ancestor of the wheat D genome, into 6 hard red winter wheat cultivars on yield and yield component traits. We used 5.2 million imputed D genome SNPs identified by the whole-genome sequencing of parental lines and the sequence-based genotyping of introgression population, including 351 BC1F3:5 lines. Phenotyping data collected from the irrigated and non-irrigated field trials revealed that up to 23% of the introgression lines (ILs) produce more grain than the parents and check cultivars. Based on 16 yield stability statistics, the yield of 12 ILs (3.4%) was stable across treatments, years, and locations; 5 of these lines were also high yielding lines, producing 9.8% more grain than the average yield of check cultivars. The most significant SNP- and haplotype-trait associations were identified on chromosome arms 2DS and 6DL for the spikelet number per spike (SNS), on chromosome arms 2DS, 3DS, 5DS, and 7DS for grain length (GL) and on chromosome arms 1DL, 2DS, 6DL, and 7DS for grain width (GW). The introgression of haplotypes from A. tauschii parents was associated with an increase in SNS, which was positively correlated with a heading date (HD), whereas the haplotypes from hexaploid wheat parents were associated with an increase in GW. We show that the haplotypes on 2DS associated with an increase in the spikelet number and HD are linked with multiple introgressed alleles of Ppd-D1 identified by the whole-genome sequencing of A. tauschii parents. Meanwhile, some introgressed haplotypes exhibited significant pleiotropic effects with the direction of effects on the yield component traits being largely consistent with the previously reported trade-offs, there were haplotype combinations associated with the positive trends in yield. The characterized repertoire of the introgressed haplotypes derived from A. tauschii accessions with the combined positive effects on yield and yield component traits in elite germplasm provides a valuable source of alleles for improving the productivity of winter wheat by optimizing the contribution of component traits to yield.

Ecogeographic signals of local adaptation in a wild relative help to identify variants associated with improved wheat performance under drought stress

“…Previously, we showed that the difference in mean yield of some Ae. tauchii introgression lines in our population reached 57% when compared to the checks under drought stress conditions (Nyine et al, 2021).…”

“…To evaluate the ability of CAAs from Ae. tauschii to improve the adaptive potential of bread wheat, we developed a wild relative introgression population using a set of 21 diverse accessions that were selected to capture the ecogeographical and allelic diversity of species (Nyine et al, 2020; Nyine et al, 2021). To facilitate comparison with parental lines, ILs in the populations were selected to match development and phenology of hexaploid wheat parents (Nyine et al, 2020).…”

“…In our previous study, we showed that 3.2% of introgression lines carrying Ae. tauschii haplotypes outperformed parental lines in drought trials (Nyine et al, 2021). Consistent with these results, several high-yielding drought tolerant cultivars have been derived from synthetic wheat lines created using Ae.…”

“…The amphiploids were then crossed with six hard red winter wheat cultivars adapted to grow in the US Great Plains to develop Ae. tauschii- wheat ILs (Nyine et al, 2020, Nyine et al, 2021). A total of 351 BC 1 F 3:5 introgression lines that had phenology similar to that of the recurrent parents were used to study the impact of introgressed CAA on the adaptative traits.…”

“…Paired-end sequences (2 x 150 bp) were generated using NovaSeq at Kansas University Medical Center and NextSeq 500 at IGF. The data were combined and processed as described by Nyine et al (2021). Missing and ungenotyped SNPs in the Ae.…”